Handling multiple spaces in the arguments, fix docker run with multiple single quote args

Author: gmarupilla

docker_run.sh

@@ -1,3 +1,23 @@
 #!/bin/bash
 
-java -classpath '/usr/local/app/vcell/lib/*' -Dvcell.installDir=/usr/local/app/vcell/installDir org.vcell.cli.CLIStandalone $1 $2 $3 $4 $5 $6
+show_help() {
+	echo "usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v]"
+	echo "  OPTIONS and ARGUMENTS:"
+	echo "    -h,--help             show this help message and exit"
+	echo ""
+	echo "    -i,--archive <arg>    Path to OMEX/COMBINE Archive file which contains one or more SED-ML encoded simulation experiments"
+	echo ""
+	echo "    -o,--out-dir <arg>    Directory to save outputs"
+	echo ""
+	echo "    -q,--quiet            Suppress all console output"
+	echo ""
+	echo "    -v,--version          Shows program's version number and exit"
+	echo ""
+	exit 1
+}
+
+if [[ $# -lt 1 ]]; then
+    show_help
+fi
+
+java -classpath '/usr/local/app/vcell/lib/*' -Dvcell.installDir=/usr/local/app/vcell/installDir org.vcell.cli.CLIStandalone "$1" "$2" "$3" "$4" "$5" "$6"